This invention relates to the design and synthesis of antisense oligonucleotides which can be administered to inhibit the replication of Hepatitis C virus in vivo or in vitro and to treat Hepatitis C virus-associated disease. These compounds can be used either prophylactically or therapeutically to reduce the severity of diseases associated with Hepatitis C virus. Oligonucleotides which are specifically hybridizable with RNA targets are disclosed.
The predominant form of hepatitis currently resulting from transfusions is not related to the previously characterized Hepatitis A virus or Hepatitis B virus and has been referred to as Non-A, Non-B Hepatitis (NANBH). NANBH currently accounts for over 90% of cases of post-transfusion hepatitis. Estimates of the frequency of NANBH in transfusion recipients range from 5%-13% for those receiving volunteer blood, or 25-54% for those receiving blood from commercial sources.
Acute NANBH, while often less severe than acute disease caused by Hepatitis A or Hepatitis B viruses, occasionally leads to severe or fulminant hepatitis. Of greater concern, progression to chronic hepatitis is much more common after NANBH than after either Hepatitis A or Hepatitis B infection. Chronic NANBH has been reported in 10%-70% of infected individuals. This form of hepatitis can be transmitted even by asymptomatic patients, and frequently progresses to malignant disease such as cirrhosis and hepatocellular carcinoma. Chronic active hepatitis, with or without cirrhosis, is seen in 44%-90% of posttransfusion hepatitis cases. Of those patients who developed cirrhosis, approximately one-fourth died of liver failure.
Chronic active NANBH is a significant problem to hemophiliacs who are dependent on blood products; 5%-11% of hemophiliacs die of chronic end-stage liver disease. Cases of NANBH other than those traceable to blood or blood products are frequently associated with hospital exposure, accidental needle stick, or tattooing. Transmission through close personal contact also occurs, though this is less common for NANBH than for Hepatitis B.
The causative agent of the majority of NANBH has recently been identified and is now referred to as Hepatitis C Virus (HCV). Houghton et al., EP Publication 318,216; Choo et al., Science 1989, 244, 359-362. Based on serological studies using recombinant DNA-generated antigens it is now clear that HCV is the causative agent of most cases of post-transfusion NANBH. Clones of cDNA prepared from nucleic acid isolated from concentrated virus particles were originally isolated based on their ability to encode polypeptides which reacted with sera from NANBH patients. These clones hybridized with RNA, but not DNA, isolated from infected liver tissue, indicating the presence of an RNA genome. Hybridization analyses and sequencing of the cDNA clones revealed that RNA present in infected liver and particles was the same polarity as that of the coding strand of the cDNAs; in other words, the virus genome is a positive or plus-strand RNA genome. EP Publication 318,216 (Houghton et al.) disclose partial genomic sequences of HCV-1, and teach recombinant DNA methods of cloning and expressing HCV sequences and HCV polypeptides, techniques of HCV immunodiagnostics, HCV probe diagnostic techniques, anti-HCV antibodies, and methods of isolating new HCV sequences. Houghton et al. also disclose additional HCV sequences and teach application of these sequences and polypeptides in immunodiagnostics, probe diagnostics, anti-HCV antibody production, PCR technology and recombinant DNA technology. The concept of using antisense polynucleotides as inhibitors of viral replication is disclosed, but no specific targets are taught. Oligomer probes and primers based on the sequences disclosed are also provided. EP Publication 419,182 (Miyamura et al.) discloses new HCV isolates J1 and J7 and use of sequences distinct from HCV-1 sequences for screens and diagnostics.
The only treatment regimen shown to be effective for the treatment of chronic NANBH is interferon-xcex1. Most NANBH patients show an improvement of clinical symptoms during interferon treatment, but relapse is observed in at least half of patients when treatment is interrupted. Significant improvements in antiviral therapy are therefore greatly desired.
It is an object of this invention to provide oligonucleotides which are capable of hybridizing with RNA of HCV to inhibit the synthesis or function of said RNA.
It is another object of this invention to provide oligonucleotides which are capable of hybridizing with RNA of HCV to inhibit replication of the virus.
It is a further object to provide oligonucleotides which can modulate the expression of HCV through antisense interaction with viral RNA.
Yet another object of this invention is to provide methods of prophylaxis, diagnostics and therapeutics for acute or chronic HCV infection.
A further object of this invention is to provide methods of prophylaxis, diagnostics and therapeutics for HCV-associated diseases.
Methods, materials and kits for detecting the presence or absence of HCV or HCV RNA in a sample suspected of containing it are further objects of the invention.
These and other objects will become apparent to persons of ordinary skill in the art from a review of the instant specification and appended claims.
In accordance with the present invention, compositions and methods for modulating the effects of HCV infection are provided. Oligonucleotides complementary to, and specifically hybridizable with, selected sequences of HCV RNA are provided. The HCV 5xe2x80x2 end hairpin loop, 5xe2x80x2 end 6-base-pair repeats, 5xe2x80x2 end untranslated region, polyprotein translation initiation codon, ORF 3 translation initiation codon, 3xe2x80x2-untranslated region, 3xe2x80x2 end palindrome region, R2 sequence and 3xe2x80x2 end hairpin loop are preferred targets. Methods for diagnosing or treating disease states by administering oligonucleotides, either alone or in combination with a pharmaceutically acceptable carrier, to animals suspected of having HCV-associated diseases are also provided.
The relationship between the target RNA and oligonucleotides complementary to at least a portion of the target, and specifically hybridizable with it, is commonly denoted as xe2x80x9cantisensexe2x80x9d. The oligonucleotides are able to inhibit the function of viral RNA by interfering with its replication, transcription into mRNA, translation into protein, packaging into viral particles or any other activity necessary to its overall biological function. The failure of the RNA to perform all or part of its function results in failure of all or a portion of the normal life cycle of the virus.
It has been found that antisense oligonucleotides designed to target viruses can be effective in diminishing viral infection. It is preferred that oligonucleotides have between about 5 and about 50 nucleotide units. It is also preferred that the oligonucleotides be specifically hybridizable with the HCV 5xe2x80x2 end hairpin loop, 5xe2x80x2 end 6-base-pair repeats, 5xe2x80x2 end untranslated region, polyprotein translation initiation codon, ORF 3 translation initiation codon, 3xe2x80x2-untranslated region, 3xe2x80x2 end palindrome region, R2 sequence or 3xe2x80x2 end hairpin loop. The oligonucleotide may be modified to increase nuclease resistance and to increase its efficacy.
In accordance with preferred embodiments, the viral RNA is interfered with to an extent sufficient to inhibit HCV infection and/or HCV replication. Thus, oligonucleotides which are capable of interacting with portions of HCV RNA are comprehended. Animals suspected of having HCV-associated disease are contacted with an oligonucleotide made in accordance with this invention. In particular, the present invention is believed to be effective in the treatment of acute and chronic HCV infections and HCV-associated disease, either prophylactically or therapeutically.
It is to be expected that differences in the RNA of HCV from different strains and from different types within a strain exist. Thus, it is believed, for example, that the regions of the various HCV strains serve essentially the same function for the respective strains and that interference with expression of the genetic information will afford similar results in the various strains. This is believed to be so even though differences in the nucleotide sequences among the strains exist.
Accordingly, nucleotide sequences set forth in the present specification will be understood to be representational for the particular strain being described. Homologous or analogous sequences for different strains of HCV are specifically contemplated as being within the scope of this invention.
Antisense oligonucleotides hold great promise as therapeutic agents for the treatment of many human diseases. In most cases, oligonucleotides complementary to specific RNA target sequences bind by Watson-Crick base pairing to pre-mRNA or mature mRNA, inhibiting the flow of genetic information from DNA to protein. In the case of RNA viruses such as HCV, oligonucleotides are designed to specifically hybridize to viral genomic RNA, mRNA, or replicative intermediate RNA, interfering with the function of the RNA such that viral replication or protein expression is modulated.
Numerous recent studies have documented the utility of antisense oligonucleotides as biochemical tools for studying target proteins. Rothenberg et al., J. Natl. Cancer Inst. 1989, 81, 1539-1544; Zon, G. Pharmaceutical Res. 1987, 5, 539-549. Because of recent advances in oligonucleotide chemistry, synthesis of nuclease-resistant oligonucleotides, and availability of types of oligonucleotides which exhibit enhanced cell uptake, it is now possible to consider the use of antisense oligonucleotides as a novel form of therapeutics.
For therapeutics, an animal suspected of having an HCV infection or HCV-associated disease is treated by administering oligonucleotides in accordance with this invention. Oligonucleotides may be formulated in a pharmaceutical composition, which may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the oligonucleotide. Pharmaceutical compositions may also include one or more active ingredients such as, for example, antimicrobial agents, antiinflammatory agents, anesthetics, and the like in addition to oligonucleotide.
The pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration may be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection.
Formulations for topical administration may include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms may also be useful.
Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders may be desirable.
Formulations for parenteral administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives.
Dosing is dependent on severity and responsiveness of the condition to be treated, but will normally be one or more doses per day, with course of treatment lasting from several days to several months or until a cure is effected or a diminution of disease state is achieved. Dosage and frequency will vary depending on, for example, body weight of patient and means of administration. Individual doses will normally range from about 0.001 mg to 500 mg, but may be higher or lower. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates.
The present invention employs oligonucleotides complementary to specific regions of HCV. RNA for antisense inhibition of HCV. In the context of this invention, the term xe2x80x9coligonucleotidexe2x80x9d refers to an oligomer or polymer of ribonucleic acid or deoxyribonucleic acid. This term includes oligomers consisting of naturally occurring bases, sugars and intersugar (backbone) linkages as well as oligomers having non-naturally occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of properties such as, for example, enhanced cellular uptake and increased stability in the presence of nucleases.
Specific examples of some preferred oligonucleotides envisioned for this invention may contain phosphorothioates, phosphotriesters, methyl phosphonates, chain alkyl or cycloalkyl intersugar linkages or short chain heteroatomic or heterocyclic intersugar linkages. Most preferred are those with CH2xe2x80x94NHxe2x80x94Oxe2x80x94CH2, CH2xe2x80x94N(CH3)xe2x80x94Oxe2x80x94CH2, CH2xe2x80x94Oxe2x80x94N(CH3)xe2x80x94CH2, CH2xe2x80x94N(CH3)xe2x80x94N(CH3)xe2x80x94CH2 and Oxe2x80x94N(CH3)xe2x80x94CH2xe2x80x94CH2 backbones (where phosphodiester is Oxe2x80x94Pxe2x80x94Oxe2x80x94CH2). Also preferred are oligonucleotides having morpholino backbone structures. Summerton, J. E. and Weller, D. D. U.S. Pat. No. 5,034,506. In other preferred embodiments, such as the protein-nucleic acid (PNA) backbone, the phosphodiester backbone of the oligonucleotide may be replaced with a polyamide backbone, the bases being bound directly or indirectly to the aza nitrogen atoms of the polyamide backbone. P. E. Nielsen, M. Egholm, R. H. Berg, O. Buchardt, Science 1991, 254, 1497. Other preferred oligonucleotides may contain alkyl and halogen-substituted sugar moieties comprising one of the following at the 2xe2x80x2 position: OH, SH, SCH3, F, OCN, O(CH2)nNH2 or O(CH2)nCH3 where n is from 1 to about 10; C1 to C10 lower alkyl, substituted lower alkyl, alkaryl or aralkyl; Cl; Br; CN; CF3; OCF3; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; SOCH3; SO2CH3; ONO2; NO2; N3; NH2; heterocycloalkyl; heterocycloalkaryl; aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleaving group; a conjugate; a reporter group; an intercalator; a group for improving the pharmacokinetic properties of an oligonucleotide; or a group for improving the pharmacodynamic properties of an oligonucleotide and other substituents having similar properties. Oligonucleotides may also have sugar mimetics such as cyclobutyls in place of the pentofuranosyl group.
All such oligonucleotides are comprehended by this invention so long as they function effectively to hybridize with HCV RNA. The oligonucleotides in accordance with this invention preferably comprise from about 5 to about 50 nucleic acid base units. It is more preferred that such oligonucleotides comprise from about 8 to 30 nucleic acid base units, and still more preferred to have from about 12 to 25 nucleic acid base units. As will be appreciated, a nucleic acid base unit is a base-sugar combination suitably bound to adjacent nucleic acid base unit through phosphodiester or other bonds.
The oligonucleotides used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including Applied Biosystems. Any other means for such synthesis may also be employed, however the actual synthesis of the oligonucleotides are well within the talents of the routineer. It is also well known to use similar techniques to prepare other oligonucleotides such as the phosphorothioates and alkylated derivatives.
In accordance with this invention, persons of ordinary skill in the art will understand that messenger RNA includes not only the sequence information to encode a protein using the three letter genetic code, but also associated ribonucleotides which form regions known to such persons as the 5xe2x80x2-untranslated region, the 3xe2x80x2-untranslated region, and the 5xe2x80x2 cap region, as well as ribonucleotides which form various secondary structures. Thus, oligonucleotides may be formulated in accordance with this invention which are targeted wholly or in part to these associated ribonucleotides as well as to the coding ribonucleotides. In preferred embodiments, the oligonucleotide is specifically hybridizable with the HCV 5xe2x80x2 end hairpin loop, 5xe2x80x2 end 6-base-pair repeats, ORF 3 translation initiation codon (all of which are contained in the 5xe2x80x2-untranslated region), polyprotein translation initiation codon, 3xe2x80x2-untranslated region, R2 region, 3xe2x80x2 hairpin loop or 3xe2x80x2 end palindrome region.
The size of the HCV genome is approximately 9400 nucleotides, with a single translational reading frame encoding a polyprotein which is subsequently processed to several structural and non-structural proteins.
Several regions of the HCV genome have been identified as antisense targets in the present invention. It should be noted that sequence availability and nucleotide numbering schemes vary from strain to strain. The 5xe2x80x2 untranslated region of HCV consists of approximately 350 nucleotides upstream of the polyprotein translation initiation codon. A hairpin loop present at nucleotides 1-22 at the 5xe2x80x2 end of the genome (HCV-1) identified herein as the xe2x80x9c5xe2x80x2 end hairpin loopxe2x80x9d is believed to serve as a recognition signal for the viral replicase or nucleocapsid proteins. Han et al., Proc. Natl. Acad. Sci. 1991, 88, 1711-1715.
Three small (12-16 amino acids each) open reading frames (ORFs) are located in the 5xe2x80x2-untranslated region of HCV RNA. These ORFs may be involved in control of translation. The ORF 3 translation initiation codon as denominated herein is found at nucleotides 315-317 of HCV-1 according to the scheme of Han et al., Proc. Natl. Acad. Sci. 1991, 88, 1711-1715; and at nucleotides-127 to -125 according to the scheme of Choo et al., Proc. Natl. Acad. Sci. 1991, 88, 2451-2455 and depicted in SEQ ID NO: 25.
The polyprotein translation initiation codon as denominated herein is an AUG sequence located at nucleotides 342-344 of HCV-1 according to Han et al., Proc. Natl. Acad. Sci. 1991, 88, 1711-1715 or at nucleotide 1-3 according to the HCV-1 numbering scheme of Choo et al., Proc. Natl. Acad. Sci. 1991, 88, 2451-2455 and SEQ ID NO: 25.
The 3xe2x80x2 untranslated region, as denominated herein, consists of nucleotides downstream of the polyprotein translation termination site (ending at nt 9037 according to Choo et al. and SEQ ID NO: 25; nt 9377 according to schemes of Han and Inchauspe as depicted in SEQ ID NO: 26). Nucleotides 9697-9716 (numbering scheme of Inchauspe for HCV-H which is depicted in SEQ ID NO: 26) at the 3xe2x80x2 terminus of the genome within the 3xe2x80x2 untranslated region can be organized into a stable hairpin loop structure identified herein as the 3xe2x80x2 hairpin loop. A short nucleotide stretch (R2) immediately upstream (nt 9691-9696 of HCV-H depicted in SEQ ID NO: 26) of the 3xe2x80x2 hairpin, and denominated herein xe2x80x9cthe R2 sequencexe2x80x9d, is thought to play a role in cyclization of the viral RNA, possibly in combination with a set of 5xe2x80x2 end 6-base-pair repeats of the same sequence at nt 23-28 and 38-43. (Inchauspe et al., Proc. Natl. Acad. Sci. 1991, 88, 10292-10296) is identified herein as xe2x80x9c5xe2x80x2 end 6-base-pair repeatxe2x80x9d. Palindrome sequences present near the 3xe2x80x2 end of the genome (nucleotides 9312-9342 according to the scheme of Takamizawa et al., J. Virol. 1991, 65, 1105-1113 depicted in SEQ ID NO: 27) are capable of forming a stable secondary structure. This is referred to herein as the 3xe2x80x2 end palindrome region.
Oligonucleotides useful in the invention are complementary to HCV RNA. Thus, the oligonucleotides in accordance with the invention preferably have one of the sequences shown in Table 1, or an effective portion thereof. It is preferred to employ any of these oligonucleotides as set forth above or any of the similar oligonucleotides, which persons of ordinary skill in the art can prepare from knowledge of the preferred antisense targets for the modulation of HCV infection.
The oligonucleotides of this invention can be used in diagnostics, therapeutics and as research reagents and kits. Since the oligonucleotides of this invention hybridize to RNA from HCV, sandwich and other assays can easily be constructed to exploit this fact. Provision of means for detecting hybridization of oligonucleotide with HCV or HCV RNA present in a sample suspected of containing it can routinely be accomplished. Such provision may include enzyme conjugation, radiolabelling or any other suitable detection systems. Kits for detecting the presence or absence of HCV may also be prepared.